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CCPEM  February 2019

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Subject:

Fw: CTFrefine/beamtilt query with Cs corrected

From:

Joseph Lyons <[log in to unmask]>

Reply-To:

Joseph Lyons <[log in to unmask]>

Date:

Wed, 13 Feb 2019 11:08:36 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (80 lines)

Answer from Takanori on a query I made in relation to Beamtilt and Cs corrected microscopes.


________________________________________
From: Takanori Nakane <[log in to unmask]>
Sent: 13 February 2019 12:01
To: Joseph Lyons
Subject: Re: CTFrefine/beamtilt query with Cs corrected

Hi,

> Is the consensus not to do
> beamtilt refinement on data from Cs-corrected microscopes?

My short answer is yes. There is no point refining beam tilt
in Cs corrected datasets (unless you are working at extremely
high resolution).

Phase errors due to beam tilt are proportional to Cs,
as indicated in Eq. 4 of
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3056894/.
Thus, the error is very small when Cs is close to zero.

The plots you attached show phase errors.
As expected, your Cs-corrected dataset does not show much
errors. When CtfRefine converts phase errors into a beam tilt,
the values are divided by a small number of Cs, sometimes
causing numerical instability and giving unnaturally large
tilts. So, your large tilt (-9 mrad) is not real. Do not worry.

Finally, if you don't mind, could you please forward this
answer to ccpem to share it to others?

Best regards,

Takanori Nakane

> Dear Takanori,
>
>
> Many thanks for such a great refinement program. I am sorry to bother you
> but I have a query related to CTFrefine and beamtilt refinement. I am
> currently working on data from a Cs corrected Titan Krios. My query is
> related to beamtilt determination on such data. Is the consensus not to do
> beamtilt refinement on data from Cs-corrected microscopes?
>
>
> Attached is a pdf of the output of CFTrefine for datasets (not the same
> sample) collected on a Cs corrected and non-Cs corrected microscope.
>
>
> The central circle in the Cs-corrected is a diffuse grey while the non-Cs
> corrected data has a gradient running across this central circle. My
> understanding is that the gradient indicates if beamtilt refinement is
> required or not - so for the Cs-corrected data one should not do beamtilt
> refinement.
>
>
> That said the output for the Cs-corrected data give quite significant
> beamtilt values for x and y compared to the non-Cs corrected data. Any
> insight into why this is the case. A Cs value of 0.01 was used for the
> Cs-corrected data and 2.7 for the non-Cs corrected data.
>
>
> Regards,
>
>
> Joe
>
>
> ?
>



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